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A permanently available molecular-beam injection setup for controlled molecules (COMO) was installed and commissioned at the small quantum systems (SQS) instrument at the European x-ray free-electron laser (EuXFEL). A b-type electrostatic deflector allows for pure state-, size-, and isomer-selected samples of polar molecules and clusters. The source provides a rotationally cold (T ≈ 1 K) and dense (ρ ≈ 108 cm-3) molecular beam with pulse durations up to 100 µs generated by a new version of the Even-Lavie valve. Here, a performance overview of the COMO setup is presented along with characterization experiments performed both with an optical laser at the Center for Free-Electron-Laser Science and with x rays at EuXFEL under burst-mode operation. COMO was designed to be attached to different instruments at the EuXFEL, in particular, the SQS and single particles, clusters, and biomolecules (SPB) instruments. This advanced controlled-molecules injection setup enables x-ray free-electron laser studies using highly defined samples with soft and hard x-ray FEL radiation for applications ranging from atomic, molecular, and cluster physics to elementary processes in chemistry and biology., (© 2024 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International (CC BY-NC-ND) license (https://creativecommons.org/licenses/by-nc-nd/4.0/).)

Radiation-induced damage of biological matter is an ubiquitous problem in nature. The influence of the hydration environment is widely discussed, but its exact role remains elusive. Utilising well defined solvated-molecule aggregates, we experimentally observed a hydrogen-bonded water molecule acting as a radiation protection agent for ionised pyrrole, a prototypical aromatic biomolecule. Pure samples of pyrrole and pyrrole(H 2 O) were outer-valence ionised and the subsequent damage and relaxation processes were studied. Bare pyrrole ions fragmented through the breaking of C-C or N-C covalent bonds. However, for pyrrole(H 2 O) + , we observed a strong protection of the pyrrole ring through the dissociative release of neutral water or by transferring an electron or proton across the hydrogen bond. Overall, a single water molecule strongly reduces the fragmentation probability and thus the persistent radiation damage of singly-ionised pyrrole.

Spatial separation of water dimers from water monomers and larger water clusters through the electric deflector is presented. A beam of water dimers with 93% purity and a rotational temperature of 1.5 K was obtained. Following strong-field ionization using a 35 fs laser pulse with a wavelength centered around 800 nm and a peak intensity of 10 14 W/cm 2 , we observed proton transfer and 46% of ionized water dimers broke apart into hydronium ions H 3 O + and neutral OH.

A knife edge for shaping a molecular beam is described to improve the spatial separation of the species in a molecular beam by the electrostatic deflector. The spatial separation of different molecular species from each other as well as from atomic seed gas is improved. The column density of the selected molecular-beam part in the interaction zone, which corresponds to higher signal rates, was enhanced by a factor of 1.5, limited by the virtual source size of the molecular beam.

Synthetic control of peptide-based supramolecular assemblies can provide molecular cues to understand protein aggregation while also inspiring the development of novel chemical biology tools to deliver cargoes inside cells. Here we show that the trans-to-cis photoisomerization of a pendant azo-group covalently attached to a Phe-Phe dipeptide can comprehensively 'turn-off' its native fibrillation propensity as well as provide an optical handle to reversibly switch the aggregate morphology from fibril to vesicle.